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Zhao K, Bai Y, Zhang Q, Zhao Z, Cao Y, Yang L, Wang N, Xu J, Wang B, Wu L, Gong X, Lin T, Wang Y, Wang W, Cai X, Yin Y, Xiong Z. Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing. BMC PLANT BIOLOGY 2023; 23:630. [PMID: 38062348 PMCID: PMC10704825 DOI: 10.1186/s12870-023-04650-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples. RESULTS In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data. CONCLUSIONS This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.
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Affiliation(s)
- Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yanbo Bai
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Qingyu Zhang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Zhen Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yao Cao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lu Yang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ni Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Junxiong Xu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Bo Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lei Wu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Xiufeng Gong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Tuanrong Lin
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Yufeng Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Wei Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Xingkui Cai
- Key Laboratory of Horticultural Plant Biology, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuhe Yin
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Mingmanit Y, Boonsrangsom T, Sujipuli K, Ratanasut K, Inthima P. Pollen viabilities and gene expression profiles across Musa genomes. AOB PLANTS 2023; 15:plad052. [PMID: 37564880 PMCID: PMC10411045 DOI: 10.1093/aobpla/plad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023]
Abstract
Banana (Musa spp.) is a major global economic fruit crop. However, cross-pollination from other Musa cultivars grown in nearby plantations results in seeded fruit that exceeds market demand. This study investigated pollen viability and germination and examined the expression profiles of pollen development-related genes across seven Musa genomes (AA, BB, AAA, BBB, AAB, ABB and ABBB). Twenty-three Musa cultivars were assessed for pollen viability using lacto-aceto-orcein and triphenyltetrazolium chloride staining methods. Results revealed that pollen viability obtained from both methods was significantly different among all the studied cultivars. Cultivars carrying BB (diploid) genomes had higher viability percentages than AA (diploid), AAA, BBB, AAB and ABB (triploid) and ABBB (tetraploid) genomes. Germination of the studied cultivars was also investigated on pollen culture medium, with results showing significant differences between the pollen of each cultivar. The best germinating cultivar was TKM (11.0 %), carrying BB genome. Expression profiles of pollen development-related genes by RT-qPCR indicated that both TPD1A and MYB80 genes were highly expressed in triploid Musa genomes but the PTC1 gene showed down-regulated expression, resulting in non-viable pollen. Pollen viability, pollen germination and pollen development-related genes differed across Musa cultivars. This knowledge will be useful for the selection of male parents for Musa cross-breeding programs. Pollen viability should also be considered when planning Musa production to avoid seeded fruit.
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Affiliation(s)
- Yonlada Mingmanit
- Department of Agricultural Science, Faculty of Agriculture Natural Resources and Environment, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
| | - Thanita Boonsrangsom
- Department of Agricultural Science, Faculty of Agriculture Natural Resources and Environment, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
- Center of Excellence in Research for Agricultural Biotechnology, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
| | - Kawee Sujipuli
- Department of Agricultural Science, Faculty of Agriculture Natural Resources and Environment, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
- Center of Excellence in Research for Agricultural Biotechnology, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
| | - Kumrop Ratanasut
- Department of Agricultural Science, Faculty of Agriculture Natural Resources and Environment, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
- Center of Excellence in Research for Agricultural Biotechnology, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
| | - Phithak Inthima
- Center of Excellence in Research for Agricultural Biotechnology, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
- Plant Tissue Culture Research Unit, Department of Biology, Faculty of Science, Naresuan University, 99 Moo 9, Tha Pho, Phitsanulok 65000, Thailand
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Soares NR, Correa CTR, da Silva JC, da Silva Negreiros JR, Techio VH, Torres GA. Comparative cytogenetics of three economically important Piper L. species from the Brazilian Amazon. PROTOPLASMA 2022; 259:1099-1108. [PMID: 34762169 DOI: 10.1007/s00709-021-01721-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The species Piper hispidinervum, Piper aduncum, and Piper affinis hispidinervum have essential oils with high levels of safrole, dillapiole, and sarisan, respectively. Safrole is important for pharmaceutical and chemical industries, while dillapiole and sarisan are promising compounds to control insects and fungi. These species are very similar morphologically and their taxonomy is controversial. Divergent hypotheses consider P. aduncum and P. hispidinervum either as a single species or as distinct taxa, while P. affinis hispidinervum is inferred to be a natural hybrid or a chemotype of P. hispidinervum. Delimiting the taxonomic boundaries would be helpful for germplasm conservation and breeding programs. This study aimed to undertake a detailed analysis of P. aduncum, P. hispidinervum, and P. affinis hispidinervum karyotype and rDNA sites. Genomic in situ hybridization (GISH) was used to establish genomic homology among species and to test the natural hybridization hypothesis for origin of P. affinis hispidinervum. Karyotype traits were similar for all three species: 2n = 26 small chromosomes, predominantly metacentric. All three species exhibited CMA+ bands on the secondary constriction of chromosome pair 4. A size-heteromorphic 35S rDNA site was co-localized with the CMA+ band. A 5S rDNA site was located in the proximal region of chromosome pair 7. The patterns of genomic hybridization revealed that the repetitive DNA fraction of the species is highly similar in terms of proportion of genome, sequence type, and distribution. Our findings did not allow us to differentiate the three species and point to the importance of deeper genomic studies to elucidate the taxonomic controversy.
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Affiliation(s)
- Nina Reis Soares
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil
| | - Caio Túlio Rodrigues Correa
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil
| | - Jhonata Costa da Silva
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil
| | | | - Vânia Helena Techio
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil
| | - Giovana Augusta Torres
- Departamento de Biologia, Instituto de Ciências Naturais, Universidade Federal de Lavas, Lavras, Minas Gerais, Brazil.
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Šimoníková D, Čížková J, Zoulová V, Christelová P, Hřibová E. Advances in the Molecular Cytogenetics of Bananas, Family Musaceae. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040482. [PMID: 35214815 PMCID: PMC8879896 DOI: 10.3390/plants11040482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 05/03/2023]
Abstract
The banana is a staple food crop and represents an important trade commodity for millions of people living in tropical and subtropical countries. The most important edible banana clones originated from natural crosses between diploid Musa balbisiana and various subspecies of M. acuminata. It is worth mentioning that evolution and speciation in the Musaceae family were accompanied by large-scale chromosome structural changes, indicating possible reasons for lower fertility or complete sterility of these vegetatively propagated clones. Chromosomal changes, often accompanied by changes in genome size, are one of the driving forces underlying speciation in plants. They can clarify the genomic constitution of edible bananas and shed light on their origin and on diversification processes in members of the Musaceae family. This article reviews the development of molecular cytogenetic approaches, ranging from classical fluorescence in situ hybridization (FISH) using common cytogenetic markers to oligo painting FISH. We discuss differences in genome size and chromosome number across the Musaceae family in addition to the development of new chromosome-specific cytogenetic probes and their use in genome structure and comparative karyotype analysis. The impact of these methodological advances on our knowledge of Musa genome evolution at the chromosomal level is demonstrated. In addition to citing published results, we include our own new unpublished results and outline future applications of molecular cytogenetics in banana research.
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Affiliation(s)
- Denisa Šimoníková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
| | - Veronika Zoulová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, 77900 Olomouc, Czech Republic
| | - Pavla Christelová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, 77900 Olomouc, Czech Republic; (D.Š.); (J.Č.); (V.Z.); (P.C.)
- Correspondence: ; Tel.: +420-585-238-713
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Cenci A, Sardos J, Hueber Y, Martin G, Breton C, Roux N, Swennen R, Carpentier SC, Rouard M. Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas. ANNALS OF BOTANY 2021; 127:7-20. [PMID: 32104882 DOI: 10.1093/aob/mcaa032/5760888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security. METHODS Using SNP markers called from RADSeq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we searched for similar events within nine AB hybrid genotypes. KEY RESULTS Recurrent homologous exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes, were unravelled with at least nine founding events (HE patterns) at the origin of ABB bananas prior to clonal diversification. Two independent founding events were found for Pisang Awak genotypes. Two HE patterns, corresponding to genotypes Pelipita and Klue Teparod, show an over-representation of B genome contribution. Three HE patterns mainly found in Indian accessions shared some recombined regions and two additional patterns did not correspond to any known subgroups. CONCLUSIONS The discovery of the nine founding events allowed an investigation of the possible routes that led to the creation of the different subgroups, which resulted in new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars, routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploids originated, and where cultivated M. balbisiana are abundant. The result of this study clarifies the classification of ABB cultivars, possibly leading to the revision of the classification of this subgroup.
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Affiliation(s)
- Alberto Cenci
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Julie Sardos
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Yann Hueber
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Guillaume Martin
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Montpellier, France
| | | | - Nicolas Roux
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Rony Swennen
- Alliance Bioversity International - CIAT, Leuven, Belgium
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, c/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | | | - Mathieu Rouard
- Alliance Bioversity International - CIAT, Montpellier, France
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6
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Cenci A, Sardos J, Hueber Y, Martin G, Breton C, Roux N, Swennen R, Carpentier SC, Rouard M. Unravelling the complex story of intergenomic recombination in ABB allotriploid bananas. ANNALS OF BOTANY 2021; 127:7-20. [PMID: 32104882 PMCID: PMC7750727 DOI: 10.1093/aob/mcaa032] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Bananas (Musa spp.) are a major staple food for hundreds of millions of people in developing countries. The cultivated varieties are seedless and parthenocarpic clones of which the ancestral origin remains to be clarified. The most important cultivars are triploids with an AAA, AAB or ABB genome constitution, with A and B genomes provided by M. acuminata and M. balbisiana, respectively. Previous studies suggested that inter-genome recombinations were relatively common in banana cultivars and that triploids were more likely to have passed through an intermediate hybrid. In this study, we investigated the chromosome structure within the ABB group, composed of starchy cooking bananas that play an important role in food security. METHODS Using SNP markers called from RADSeq data, we studied the chromosome structure of 36 ABB genotypes spanning defined taxonomic subgroups. To complement our understanding, we searched for similar events within nine AB hybrid genotypes. KEY RESULTS Recurrent homologous exchanges (HEs), i.e. chromatin exchanges between A and B subgenomes, were unravelled with at least nine founding events (HE patterns) at the origin of ABB bananas prior to clonal diversification. Two independent founding events were found for Pisang Awak genotypes. Two HE patterns, corresponding to genotypes Pelipita and Klue Teparod, show an over-representation of B genome contribution. Three HE patterns mainly found in Indian accessions shared some recombined regions and two additional patterns did not correspond to any known subgroups. CONCLUSIONS The discovery of the nine founding events allowed an investigation of the possible routes that led to the creation of the different subgroups, which resulted in new hypotheses. Based on our observations, we suggest different routes that gave rise to the current diversity in the ABB cultivars, routes involving primary AB hybrids, routes leading to shared HEs and routes leading to a B excess ratio. Genetic fluxes took place between M. acuminata and M. balbisiana, particularly in India, where these unbalanced AB hybrids and ABB allotriploids originated, and where cultivated M. balbisiana are abundant. The result of this study clarifies the classification of ABB cultivars, possibly leading to the revision of the classification of this subgroup.
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Affiliation(s)
- Alberto Cenci
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Julie Sardos
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Yann Hueber
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Guillaume Martin
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR AGAP, Montpellier, France
| | | | - Nicolas Roux
- Alliance Bioversity International - CIAT, Montpellier, France
| | - Rony Swennen
- Alliance Bioversity International - CIAT, Leuven, Belgium
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- International Institute of Tropical Agriculture, c/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | | | - Mathieu Rouard
- Alliance Bioversity International - CIAT, Montpellier, France
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Dehery SK, Panda E, Saha PR, Sinha RK, Das AB. Chromosome diversity and karyotype asymmetry analysis in four cultivated triploid and three diploid wild genotypes of Musa from North-East India. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00334-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Das AB, Dehery SK, Kiran, Jena SN, Sinha RK. A New Seeded Diploid Accession of Musa laterita of Section Rhodochlamys From Gangtok, Sikkim, India with Morphology, Chromosome Number and Genome Size. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Anath Bandhu Das
- Molecular Cytogenetics Laboratory, Department of Botany, Utkal University
| | | | - Kiran
- CSIR-National Botanical Research Institute
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Konan NO, Mergeai G. Relationship between meiotic behaviour and fertility in backcross-1 derivatives of the [( Gossypium hirsutum × G. thurberi) 2 × G. longicalyx] trispecies hybrid. COMPARATIVE CYTOGENETICS 2020; 14:75-95. [PMID: 32047586 PMCID: PMC7000483 DOI: 10.3897/compcytogen.v14i1.47231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/04/2020] [Indexed: 06/10/2023]
Abstract
Wild cotton species are an important source of desirable genes for genetic improvement of cultivated cotton Gossypium hirsutum Linnaeus, 1763. For the success of such an improvement, chromosome pairings and recombinations in hybrids are fundamental. The wild African species G. longicalyx Hutchinson & Lee, 1958 could be used as donor of the desirable trait of fiber fineness. Twelve BC1 plants obtained from the backcrossing of [(G. hirsutum × G. thurberi Todaro, 1877)2 × G. longicalyx] (AhDhD1F1, 2n = 4x = 52) trispecies hybrid (HTL) by G. hirsutum (cv. C2) (AhAhDhDh, 2n = 4x = 52) were investigated for meiotic behaviour and plant fertility. Their chromosome associations varied as follows: (2.5 to 11.5) I + (17 to 22) II + (0.31 to 1.93) III + (0.09 to 1.93) IV + (0 to 0.07) V + (0 to 0.14) VI. Their pollen fertility ranged from 4.67 to 32.10 %. Only four BC1 plants produced a few seeds through self-pollination. The remaining BC1 were totally self-sterile and usually presented the highest number of univalents. All BC1 materials produced BC2 seeds (0.44 to 6.50 seeds per backcross) with the number of seeds negatively correlated with the number of univalents (R2 = 0.45, P < 0.05). Most BC1 plants gave significantly finer fiber compared to the cultivated G. hirsutum. SSR markers showed a segregation of wild alleles among the backcross derivatives and Genomic in situ hybridization (GISH) revealed presence of entire chromosomes of G. longicalyx as well as recombinant chromosomes in the backcross derivatives. The significance and details of these results are presented and the prospects of successfully exploiting these plant materials are discussed.
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Affiliation(s)
- N’guessan Olivier Konan
- Gembloux Agro-Bio Tech, Liège University, Tropical agriculture Unit, 2 passage des Déportés, B-5030 Gembloux, BelgiumLiège UniversityGemblouxBelgium
- Jean Lorougnon Guédé University, Agroforestry Unit, BP 150, Cote D’ivoireJean Lorougnon Guédé UniversityDaloaCote d'Ivoire
| | - Guy Mergeai
- Gembloux Agro-Bio Tech, Liège University, Tropical agriculture Unit, 2 passage des Déportés, B-5030 Gembloux, BelgiumLiège UniversityGemblouxBelgium
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Dupouy M, Baurens FC, Derouault P, Hervouet C, Cardi C, Cruaud C, Istace B, Labadie K, Guiougou C, Toubi L, Salmon F, Mournet P, Rouard M, Yahiaoui N, Lemainque A, Martin G, D’Hont A. Two large reciprocal translocations characterized in the disease resistance-rich burmannica genetic group of Musa acuminata. ANNALS OF BOTANY 2019; 124:319-329. [PMID: 31241133 PMCID: PMC6758587 DOI: 10.1093/aob/mcz078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/09/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND AND AIMS Banana cultivars are derived from hybridizations involving Musa acuminata subspecies. The latter diverged following geographical isolation in distinct South-east Asian continental regions and islands. Observation of chromosome pairing irregularities in meiosis of hybrids between these subspecies suggested the presence of large chromosomal structural variations. The aim of this study was to characterize such rearrangements. METHODS Marker (single nucleotide polymorphism) segregation in a self-progeny of the 'Calcutta 4' accession and mate-pair sequencing were used to search for chromosomal rearrangements in comparison with the M. acuminata ssp. malaccensis genome reference sequence. Signature segment junctions of the revealed chromosome structures were identified and searched in whole-genome sequencing data from 123 wild and cultivated Musa accessions. KEY RESULTS Two large reciprocal translocations were characterized in the seedy banana M. acuminata ssp. burmannicoides 'Calcutta 4' accession. One consisted of an exchange of a 240 kb distal region of chromosome 2 with a 7.2 Mb distal region of chromosome 8. The other involved an exchange of a 20.8 Mb distal region of chromosome 1 with a 11.6 Mb distal region of chromosome 9. Both translocations were found only in wild accessions belonging to the burmannicoides/burmannica/siamea subspecies. Only two of the 87 cultivars analysed displayed the 2/8 translocation, while none displayed the 1/9 translocation. CONCLUSION Two large reciprocal translocations were identified that probably originated in the burmannica genetic group. Accurate characterization of these translocations should enhance the use of this disease resistance-rich burmannica group in breeding programmes.
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Affiliation(s)
- Marion Dupouy
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Paco Derouault
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Céline Cardi
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Corinne Cruaud
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Benjamin Istace
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | | | | | | | - Pierre Mournet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Nabila Yahiaoui
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Arnaud Lemainque
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Angélique D’Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- For correspondence. E-mail
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11
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Brisibe EA, Ekanem NG. Ploidy level and nucleotide variations in inflorescence dichotomous cultivars of plantain (Musa spp. AAB genome). BMC Genomics 2019; 20:713. [PMID: 31521108 PMCID: PMC6744660 DOI: 10.1186/s12864-019-6083-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/06/2019] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Inflorescence dichotomy in Musa species is a rare developmental event which leads to the production of multiple bunches on a single pseudostem at fruiting. In spite of its fascinating attraction and seductive appeal, little is known about the cytogenetic basis and molecular mechanisms that could be ascribed to this phenomenon. To bridge this gap in information, an integrative approach using cytological fingerprinting and DNA ploidy level profiling (based on chromosome counting and flow cytometry) were assayed on five inflorescence dichotomous plantain varieties and a single-bunching cultivar that served as control. This was done to assess the number and behaviour of chromosomes on the one hand and single nucleotide polymorphisms identified during analysis of nucleotide variations on the other. RESULTS Chromosomes stained with aceto-orcein were very tiny, compact, metacentric and acrocentric, and differed both in number and ploidy level between the inflorescence dichotomous and single-bunching cultivars. The dichotomous plantains were mainly diploid (2n = 2x = 22) while the single-bunching 'Agbagba' cultivar was consistently a triploid (2n = 3x = 33), as revealed by histological chromosome counting and flow cytometry, implying that there was a high incidence of genomic divergence on account of ploidy variations among the different Musa cultivars. Molecular genotyping using single nucleotide polymorphisms detected on the GTPase-protein binding gene of the leaf tissue gene complex provided further evidence indicating that differences in the number of bunches among the inflorescence dichotomous cultivars could be ascribed to nucleotide diversity that was elicited by changes in amino acid sequences in the genome of the crops. Non-synonymous nucleotide substitutions resulted mainly from transversion (from purine to pyramidine and vice versa), tacitly implying that these changes were crucial and promoted a cascade of reactions in the genome that were, probably, responsible for the non-persistence of the dichotomization event(s) or the reversals in the bunch phenotype detected among the inflorescence dichotomous cultivars. CONCLUSIONS This is the first report of cytogenetic fingerprints and nucleotide diversity detection among single- and multiple-bunching Musa cultivars. A clear distinction between the two groups was found that is indicative of variations both in ploidy level and nucleotide sequences. The pattern of single nucleotide polymorphisms provided profound clues suggesting that there was a high incidence of genomic divergence, due to random and unstable genetic events that were triggered by frequent spontaneous somatic mutations.
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Affiliation(s)
- Ebiamadon Andi Brisibe
- Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
- Bio-therapeutics/Bio-industrial and Plant Cell and Tissue Culture Research Laboratory, ACR Technologies Limited, 124 MCC Road, Calabar, Nigeria
| | - Norah Godwin Ekanem
- Department of Crop Science, Faculty of Agriculture, University of Uyo, Uyo, Nigeria
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12
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Baurens FC, Martin G, Hervouet C, Salmon F, Yohomé D, Ricci S, Rouard M, Habas R, Lemainque A, Yahiaoui N, D'Hont A. Recombination and Large Structural Variations Shape Interspecific Edible Bananas Genomes. Mol Biol Evol 2019; 36:97-111. [PMID: 30403808 PMCID: PMC6340459 DOI: 10.1093/molbev/msy199] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Admixture and polyploidization are major recognized eukaryotic genome evolutionary processes. Their impacts on genome dynamics vary among systems and are still partially deciphered. Many banana cultivars are triploid (sometimes diploid) interspecific hybrids between Musa acuminata (A genome) and M. balbisiana (B genome). They have no or very low fertility, are vegetatively propagated and have been classified as “AB,” “AAB,” or “ABB” based on morphological characters. We used NGS sequence data to characterize the A versus B chromosome composition of nine diploid and triploid interspecific cultivars, to compare the chromosome structures of A and B genomes and analyze A/B chromosome segregations in a polyploid context. We showed that interspecific recombination occurred frequently between A and B chromosomes. We identified two large structural variations between A and B genomes, a reciprocal translocation and an inversion that locally affected recombination and led to segregation distortion and aneuploidy in a triploid progeny. Interspecific recombination and large structural variations explained the mosaic genomes observed in edible bananas. The unprecedented resolution in deciphering their genome structure allowed us to start revisiting the origins of banana cultivars and provided new information to gain insight into the impact of interspecificity on genome evolution. It will also facilitate much more effective assessment of breeding strategies.
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Affiliation(s)
- Franc-Christophe Baurens
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Frédéric Salmon
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,CIRAD, UMR AGAP, F-97130 Capesterre Belle Eau, Guadeloupe, France
| | | | - Sébastien Ricci
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,CIRAD, UMR AGAP, F-97130 Capesterre Belle Eau, Guadeloupe, France.,CARBAP, Bonanjo, Douala, Cameroon
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, Cedex 5, France
| | - Remy Habas
- CIRAD, UMR BGPI, F-34398 Montpellier, France.,BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Arnaud Lemainque
- Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François-Jacob, Genoscope, Evry, France
| | - Nabila Yahiaoui
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, F-34398 Montpellier, France.,AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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13
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Drapal M, de Carvalho EB, Rouard M, Amah D, Sardos J, Van den Houwe I, Brown A, Roux N, Swennen R, Fraser PD. Metabolite profiling characterises chemotypes of Musa diploids and triploids at juvenile and pre-flowering growth stages. Sci Rep 2019; 9:4657. [PMID: 30874619 PMCID: PMC6420674 DOI: 10.1038/s41598-019-41037-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/22/2019] [Indexed: 11/16/2022] Open
Abstract
Bananas (Musa spp.) are consumed worldwide as dessert and cooking types. Edible banana varieties are for the most part seedless and sterile and therefore vegetatively propagated. This confers difficulties for breeding approaches against pressing biotic and abiotic threats and for the nutritional enhancement of banana pulp. A panel of banana accessions, representative of the diversity of wild and cultivated bananas, was analysed to assess the range of chemotypes available globally. The focus of this assessment was banana leaves at two growth stages (juvenile and pre-flowering), to see when during the plant growth metabolic differences can be established. The metabolic data corresponded to genomic trends reported in previous studies and demonstrated a link between metabolites/pathways and the genomes of M. acuminata and M. balbisiana. Furthermore, the vigour and resistance traits of M. balbisiana was connected to the phenolic composition and showed differences with the number of B genes in the hybrid accessions. Differences in the juvenile and pre-flowering data led to low correlation between the growth stages for prediction purposes.
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Affiliation(s)
- Margit Drapal
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | | | - Mathieu Rouard
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Delphine Amah
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Julie Sardos
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | | | - Allan Brown
- International Institute of Tropical Agriculture, Arusha, Tanzania
| | - Nicolas Roux
- Bioversity France, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Rony Swennen
- International Institute of Tropical Agriculture, Arusha, Tanzania.,Bioversity International, W. De Croylaan 42, 3001, Heverlee, Belgium.,Department of Biosystem, KU Leuven University, Oude Markt 13 - bus 5005, 3000, Leuven, Belgium
| | - Paul D Fraser
- School of Biological Sciences, Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK.
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14
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Tonosaki K, Osabe K, Kawanabe T, Fujimoto R. The importance of reproductive barriers and the effect of allopolyploidization on crop breeding. BREEDING SCIENCE 2016; 66:333-49. [PMID: 27436943 PMCID: PMC4902455 DOI: 10.1270/jsbbs.15114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/25/2016] [Indexed: 05/04/2023]
Abstract
Inter-specific hybrids are a useful source for increasing genetic diversity. Some reproductive barriers before and/or after fertilization prevent production of hybrid plants by inter-specific crossing. Therefore, techniques to overcome the reproductive barrier have been developed, and have contributed to hybridization breeding. In recent studies, identification of molecules involved in plant reproduction has been studied to understand the mechanisms of reproductive barriers. Revealing the molecular mechanisms of reproductive barriers may allow us to overcome reproductive barriers in inter-specific crossing, and to efficiently produce inter-specific hybrids in cross-combinations that cannot be produced through artificial techniques. Inter-specific hybrid plants can potentially serve as an elite material for plant breeding, produced through the merging of genomes of parental species by allopolyploidization. Allopolyploidization provides some benefits, such as heterosis, increased genetic diversity and phenotypic variability, which are caused by dynamic changes of the genome and epigenome. Understanding of allopolyploidization mechanisms is important for practical utilization of inter-specific hybrids as a breeding material. This review discusses the importance of reproductive barriers and the effect of allopolyploidization in crop breeding programs.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University,
641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813,
Japan
- Corresponding author (e-mail: )
| | - Kenji Osabe
- Okinawa Institute of Science and Technology,
1919-1 Tancha, Onna-son, Kunigami, Okinawa 904-0495,
Japan
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe 657-8501,
Japan
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15
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Jang TS, Weiss-Schneeweiss H. Formamide-Free Genomic in situ Hybridization Allows Unambiguous Discrimination of Highly Similar Parental Genomes in Diploid Hybrids and Allopolyploids. Cytogenet Genome Res 2015; 146:325-31. [PMID: 26492445 DOI: 10.1159/000441210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2015] [Indexed: 11/19/2022] Open
Abstract
Polyploidy and hybridization play an important role in plant diversification and speciation. The application of genomic in situ hybridization (GISH) allows the identification of parental genomes in hybrids, thus elucidating their origins and allowing for analysis of their genomic evolution. The performance of GISH depends on the similarity of the parental genomes and on the age of hybrids. Here, we present the formamide-free GISH (ff-GISH) protocol applied to diploid and polyploid hybrids of monocots (Prospero, Hyacinthaceae) and dicots (Melampodium, Asteraceae) differing in similarity of the parental genomes and in chromosome and genome sizes. The efficiency of the new protocol is compared to the standard GISH protocol. As a result, ff-GISH allowed efficient labeling and discrimination of the parental chromosome sets in diploid and allopolyploid hybrids in Prospero autumnale species complex. In contrast, the standard GISH protocol failed to differentiate the parental genomes due to high levels of similar repetitive DNA. Likewise, an unambiguous identification of parental genomes in allotetraploid Melampodium nayaritense (Asteraceae) was possible after ff-GISH, whereas the standard GISH hybridization performance was suboptimal. The modified method is simple and non-toxic and allows the discrimination of very similar parental genomes in hybrids. This method lends itself to modifications and improvements and can also be used for FISH.
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Affiliation(s)
- Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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16
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Ortiz R, Swennen R. From crossbreeding to biotechnology-facilitated improvement of banana and plantain. Biotechnol Adv 2014; 32:158-69. [DOI: 10.1016/j.biotechadv.2013.09.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 12/30/2022]
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17
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Davey MW, Gudimella R, Harikrishna JA, Sin LW, Khalid N, Keulemans J. "A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids". BMC Genomics 2013; 14:683. [PMID: 24094114 PMCID: PMC3852598 DOI: 10.1186/1471-2164-14-683] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 09/24/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Modern banana cultivars are primarily interspecific triploid hybrids of two species, Musa acuminata and Musa balbisiana, which respectively contribute the A- and B-genomes. The M. balbisiana genome has been associated with improved vigour and tolerance to biotic and abiotic stresses and is thus a target for Musa breeding programs. However, while a reference M. acuminata genome has recently been released (Nature 488:213-217, 2012), little sequence data is available for the corresponding B-genome.To address these problems we carried out Next Generation gDNA sequencing of the wild diploid M. balbisiana variety 'Pisang Klutuk Wulung' (PKW). Our strategy was to align PKW gDNA reads against the published A-genome and to extract the mapped consensus sequences for subsequent rounds of evaluation and gene annotation. RESULTS The resulting B-genome is 79% the size of the A-genome, and contains 36,638 predicted functional gene sequences which is nearly identical to the 36,542 of the A-genome. There is substantial sequence divergence from the A-genome at a frequency of 1 homozygous SNP per 23.1 bp, and a high degree of heterozygosity corresponding to one heterozygous SNP per 55.9 bp. Using expressed small RNA data, a similar number of microRNA sequences were predicted in both A- and B-genomes, but additional novel miRNAs were detected, including some that are unique to each genome. The usefulness of this B-genome sequence was evaluated by mapping RNA-seq data from a set of triploid AAA and AAB hybrids simultaneously to both genomes. Results for the plantains demonstrated the expected 2:1 distribution of reads across the A- and B-genomes, but for the AAA genomes, results show they contain regions of significant homology to the B-genome supporting proposals that there has been a history of interspecific recombination between homeologous A and B chromosomes in Musa hybrids. CONCLUSIONS We have generated and annotated a draft reference Musa B-genome and demonstrate that this can be used for molecular genetic mapping of gene transcripts and small RNA expression data from several allopolyploid banana cultivars. This draft therefore represents a valuable resource to support the study of metabolism in inter- and intraspecific triploid Musa hybrids and to help direct breeding programs.
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Affiliation(s)
- Mark W Davey
- Laboratory of Fruit Breeding and Biotechnology, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, box 2427B-3001, Heverlee, Leuven, Belgium
| | - Ranganath Gudimella
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Lee Wan Sin
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Norzulaani Khalid
- Centre for Research in Biotechnology for Agriculture and Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Johan Keulemans
- Laboratory of Fruit Breeding and Biotechnology, Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit Leuven, Willem de Croylaan 42, box 2427B-3001, Heverlee, Leuven, Belgium
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18
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de Jesus ON, Silva SDOE, Amorim EP, Ferreira CF, de Campos JMS, Silva GDG, Figueira A. Genetic diversity and population structure of Musa accessions in ex situ conservation. BMC PLANT BIOLOGY 2013; 13:41. [PMID: 23497122 PMCID: PMC3636076 DOI: 10.1186/1471-2229-13-41] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/22/2013] [Indexed: 05/06/2023]
Abstract
BACKGROUND Banana cultivars are mostly derived from hybridization between wild diploid subspecies of Musa acuminata (A genome) and M. balbisiana (B genome), and they exhibit various levels of ploidy and genomic constitution. The Embrapa ex situ Musa collection contains over 220 accessions, of which only a few have been genetically characterized. Knowledge regarding the genetic relationships and diversity between modern cultivars and wild relatives would assist in conservation and breeding strategies. Our objectives were to determine the genomic constitution based on Internal Transcribed Spacer (ITS) regions polymorphism and the ploidy of all accessions by flow cytometry and to investigate the population structure of the collection using Simple Sequence Repeat (SSR) loci as co-dominant markers based on Structure software, not previously performed in Musa. RESULTS From the 221 accessions analyzed by flow cytometry, the correct ploidy was confirmed or established for 212 (95.9%), whereas digestion of the ITS region confirmed the genomic constitution of 209 (94.6%). Neighbor-joining clustering analysis derived from SSR binary data allowed the detection of two major groups, essentially distinguished by the presence or absence of the B genome, while subgroups were formed according to the genomic composition and commercial classification. The co-dominant nature of SSR was explored to analyze the structure of the population based on a Bayesian approach, detecting 21 subpopulations. Most of the subpopulations were in agreement with the clustering analysis. CONCLUSIONS The data generated by flow cytometry, ITS and SSR supported the hypothesis about the occurrence of homeologue recombination between A and B genomes, leading to discrepancies in the number of sets or portions from each parental genome. These phenomenons have been largely disregarded in the evolution of banana, as the "single-step domestication" hypothesis had long predominated. These findings will have an impact in future breeding approaches. Structure analysis enabled the efficient detection of ancestry of recently developed tetraploid hybrids by breeding programs, and for some triploids. However, for the main commercial subgroups, Structure appeared to be less efficient to detect the ancestry in diploid groups, possibly due to sampling restrictions. The possibility of inferring the membership among accessions to correct the effects of genetic structure opens possibilities for its use in marker-assisted selection by association mapping.
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Affiliation(s)
- Onildo Nunes de Jesus
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil
- Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
- EMBRAPA Mandioca Fruticultura, R. Embrapa s/n, Cruz das Almas, BA, 44380-000, Brazil
| | | | - Edson Perito Amorim
- EMBRAPA Mandioca Fruticultura, R. Embrapa s/n, Cruz das Almas, BA, 44380-000, Brazil
| | | | | | - Gabriela de Gaspari Silva
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil
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19
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Jeridi M, Perrier X, Rodier-Goud M, Ferchichi A, D'Hont A, Bakry F. Cytogenetic evidence of mixed disomic and polysomic inheritance in an allotetraploid (AABB) Musa genotype. ANNALS OF BOTANY 2012; 110:1593-606. [PMID: 23087127 PMCID: PMC3503499 DOI: 10.1093/aob/mcs220] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 09/10/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Edible bananas originated mainly from two wild species, Musa acuminata Colla (AA) and Musa balbisiana Colla (BB), and triploid cultivars with an AAA, AAB or ABB genome are the most widely used. In the present study, chromosome pairing affinities are investigated in a sterile AB Indian variety and in its fertile colchicine-induced allotetraploid (AABB) derivative to determine the inheritance pattern of the tetraploid genotype. The potential implications of interspecific recombination and chromosomal composition of diploid gametes for Musa improvement are presented. METHODS The pairing of different chromosome sets at diploid and tetraploid levels was investigated through a combination of conventional cytogenetic and genomic in-situ hybridization (GISH) analyses of meiotic chromosomes, leading to a likelihood model of the pairing behaviour. GISH analysis of mitotic chromosomes was also conducted to reveal the chromosome constitution of hybrids derived from crosses involving the allotetraploid genotype. KEY RESULTS Analysis of chromosome associations at both ploidy levels suggested that the newly formed allotetraploid behaves as a 'segmental allotetraploid' with three chromosome sets in a tetrasomic pattern, three sets in a likely disomic pattern and the five remaining sets in an intermediate pattern. Balanced and unbalanced diploid gametes were detected in progenies, with the chromosome constitution appearing to be more homogenous in pollen than in ovules. CONCLUSIONS Colchicine-induced allotetraploids in Musa provide access to the genetic background of natural AB varieties. The segmental inheritance pattern exhibited by the AABB allotetraploid genotype implies chromosome exchanges between M. acuminata and M. balbisiana species and opens new horizons for reciprocal transfer of valuable alleles.
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Affiliation(s)
- Mouna Jeridi
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
- Institut des Régions Arides (IRA), 4119 Médenine, Tunisia
| | - Xavier Perrier
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
| | - Marguerite Rodier-Goud
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
| | - Ali Ferchichi
- Institut des Régions Arides (IRA), 4119 Médenine, Tunisia
| | - Angélique D'Hont
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
| | - Frédéric Bakry
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP, Avenue Agropolis, F-34398 Montpellier, France
- For correspondence. E-mail
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20
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D'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci AM, Weissenbach J, Ruiz M, Glaszmann JC, Quétier F, Yahiaoui N, Wincker P. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 2012; 488:213-7. [PMID: 22801500 DOI: 10.1038/nature11241] [Citation(s) in RCA: 610] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 05/18/2012] [Indexed: 01/17/2023]
Abstract
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.
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Affiliation(s)
- Angélique D'Hont
- Centre de coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, F-34398 Montpellier, France. angelique.d’
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